createCompoundCmatrix: Builds a compound C matrix.

Description

Uses clonality object, and environmental transition objects to construct a matrix defining probabilities for transitions between sizes due to clonal reporudction given both a continuous state (e.g. size) and environmental state, as well as a discrete stage if necessary. Currently only pre-census clonal reproduction can be handled.

Usage

createCompoundCmatrix(nEnvClass = 2, nBigMatrix = 50,
minSize = -1, maxSize = 50, envMatrix, clonalObj, integrateType, correction)

Arguments

nEnvClass

numeric, number of environmental classes, defaults to 2.

nBigMatrix

numeric, number of size bins in the P matrix, defaults to 50.

minSize

numeric, minimum size of the P matrix, defaults to -1.

maxSize

numeric, maximum size of the P matrix, defaults to 50.

envMatrix

envMatrix object defining transitions between environmental states for each size.

clonalObj

clonality object.

integrateType

integration type, defaults to "midpoint" (which uses probability density function); other option is "cumul" (which uses the cumulative density function).

correction

correction type, defaults to none. The first option is constant which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for total fertility at that size. The second option is

Value

an object of class IPMmatrix with dimensions nBigMatrix*nEnvClass, or if discrete transitions exist (nBigMatrix+nDisc)*nEnvClass

References

For information on C matrix: Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p110-112.

For midpoint: Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.

For multiple-vital rate integration on fecundity: Yang, Jongejans, Yang & Bishop. 2011. The effect of consumers and mutualists of Vaccinum membranaceum at Mount St. Helens: dependence on successional context. PLoS One 10, p1-11.

Examples

Run this code

## See createCompoundFmatrix for examples